Evaluation of the linkage-disequilibrium method for the estimation of effective population size when generations overlap: an empirical case

Background: Within the genetic methods for estimating effective population size (Ne), the method based on linkage disequilibrium (LD) has advantages over other methods, although its accuracy when applied to populations with overlapping generations is a matter of controversy. It is also unclear the best way to account for mutation and sample size when this method is implemented. Here we have addressed the applicability of this method using genome-wide information when generations overlap by profiting from having available a complete and accurate pedigree from an experimental population of Iberian pigs. Precise pedigree-based estimates of Ne were considered as a baseline against which to compare LD-based estimates. Methods: We assumed six different statistical models that varied in the adjustments made for mutation and sample size. The approach allowed us to determine the most suitable statistical model of adjustment when the LD method is used for species with overlapping generations. A novel approach used here was to treat different generations as replicates of the same population in order to assess the error of the LD-based Ne estimates. Results: LD-based Ne estimates obtained by estimating the mutation parameter from the data and by correcting sample size using the 1/2n term were the closest to pedigree-based estimates. The Ne at the time of the foundation of the herd (26 generations ago) was 20.8 +/- 3.7 (average and SD across replicates), while the pedigree-based estimate was 21. From that time on, this trend was in good agreement with that followed by pedigree-based Ne. Conclusions: Our results showed that when using genome-wide information, the LD method is accurate and broadly applicable to small populations even when generations overlap. This supports the use of the method for estimating Ne when pedigree information is unavailable in order to effectively monitor and manage populations and to early detect population declines. To our knowledge this is the first study using replicates of empirical data to evaluate the applicability of the LD method by comparing results with accurate pedigree-based estimates.